What is Phoenix?
Phoenix is a variant annotation and filtering tool capable of processing billions of variants from multiple species.
How to Use Phoenix (Getting Started)
General Flow:
- Build Your Cohort: Select the specific samples you want to analyze.
- Filter Variants: Narrow down the list of variants based on desired criteria.
- Explore Individual Variants: Attach custom notes or metadata to variants. Browse variant location with UCSC Genome Browser.
- Add Variants to Cart: Move the variants you want to keep to your final selection cart.
- Iterate: Repeat steps 2-4 to refine your selection.
- Save and Manage Your Work: View your final cart selection and save it for future use or export.
Specific Steps:
Step 1: Build Your Cohort
The cohort is the starting point for all analysis. It defines the set of variants you will work with.
Step 2: Filter Variants
After building your cohort, you will refine the millions of genetic variants down to a manageable list using various filtering tools:
- Basic Column Filters: Most columns can be filtered based on their types with common comparators.
- Advanced Filters (Filter Panel): A set of frequently used filters with customized selectors. Also a place to filter by fields not present in the table (e.g., Regions and Phenotypes).
- AI Filtering: An experimental feature to help set column filters with natural language. [Video tutorial coming soon]
Step 3: Explore Individual Variants
- Adding annotations: You can write annotation cards for any variants. Those annotations will be displayed in other variants if they match the same scope (e.g., same species or region).. Select a variant and click the "Add Annotation" button to create a custom note. [Video tutorial coming soon]
- Viewing annotations: Annotations appear on matching variants throughout your analysis.
- Open a variant location with UCSC Genome Browser:
- From the Target Selection Page:
- From the Variant Details Page
Step 4: Add Variants to Your Cart
- Add a single variant to the cart: Select the variant's row and click the "Add to Cart" icon.
- Add all filtered variants to cart: Use the bulk action button to add the entire filtered list. (Note: This action has a limit of 1,000 variants per batch.)
Step 6: Saving and Managing Your Work
Saving Your Variant Selection:
- Navigate to the Cart view.
- Review your final list of variants.
- Click "Save Selection" and provide a descriptive name for your file.
Manage Annotations
- You can view, edit, and delete all your annotations in one place. [Video tutorial coming soon]
Continue Work from a Previously Saved State:
- You can load a saved cohort from your workspace to continue filtering.
Finding Your Saved Variants:
FAQ (Frequently Asked Questions)
This section will be populated with common questions sourced from messages and Slack.
Can I arrange and resize columns in Target Selection?
You sure can! Click here for tips and tricks for customizing tables. [Video tutorial coming soon]